Dataset: Microorganisms associated with pyrosomes

Name: Microorganisms associated with pyrosomes
Published: 2024-04-26
Keywords: pyrosomes, microorganisms, Synechococcus, oceans

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Spatial Extent: N:44.652141 E:-124.589313 S:44.651756 W:-125.117573

Northern California Current System

Temporal Extent: 2018-07-09 - 2018-07-11

Project:

Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey (Gelatinous Grazer Feeding)

Co-Principal Investigator:

Anne W. Thompson (Portland State University, PSU)

Contact:

Anne W. Thompson (Portland State University, PSU)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-04-26

Restricted:

Validated:

Current State:

Data not available

16S rRNA sequencing pyrosome-associated microorganisms

Abstract:

Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry.

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Methods & Sampling

Pyrosomes and seawater were collected from the NCC, off the Oregon Coast, in July 2018, near the peak of a multiyear bloom of P. atlanticum. Samples were collected from the R/V Sally Ride (SR1810) along the Newport Hydrographic Line. Station D5 (Cast 20, 44.652141N; 125.117573W) was sampled on July 9, 2018 in the presence of a strong temperature gradient in the top 20 meters and a chlorophyll peak at 17 meters. Station D3 (Cast 26, 44.651756N; 124.589313W) was sampled on July 11, 2018 in the presence of a mixed layer depth of 15 meters and a chlorophyll peak at the base of the mixed layer.

Data Processing Description

DNA extraction was done using the DNeasy Plant Tissue Mini Kit (Qiagen) with the following modifications. Pyrosome tissue was ground with a sterile pestle (Axygen, Tewksbury, USA) for 3 minutes prior to extraction. Seawater and pyrosome samples were lysed by bead beating with 0.55 mm and 0.25 mm sterile glass beads at 30 Hz for 2 minutes after addition of lysis buffer, freeze-fractured 3 times, incubated with Proteinase K (VWR Chemicals, Solon, OH, USA) at 20 mg/mL for 1 hour at 55 ˚C, and incubated with RNase A at 100 mg/mL for 10 minutes at 65 ˚C. To minimize amplification of eukaryotic host DNA, the primer pair 515F‐Y/806R was chosen to amplify the 16S rRNA V4 hypervariable region with conditions as published. Reactions were performed with 0.5-2 ng of DNA using the QuantaBio 5Prime HotMasterMix (Qiagen Beverly, MA, USA). The Agilent High Sensitivity Kit in the Bioanalyzer (Agilent Technologies, Waldbronn, Germany) confirmed amplicon size. Triplicate reactions from each sample were pooled and paired-end sequenced with Illumina MiSeq v.3 (Illumina, San Diego, USA).

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851412

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
SR1810	S18	2018-07-06	R/V Sally Ride	Robert K. Cowen (Chief Scientist)	data info

Instruments

CTD - profiler

Supplied Name: Niskin CTD Rosette for seawater

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

MOCNESS

Supplied Name: MOCNESS for animals

Supplied Description:

Instrument Type

Generic Name: MOCNESS

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/

Generic Description:

The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. There are currently 8 different sizes of MOCNESS in existence which are designed for capture of different size ranges of zooplankton and micro-nekton Each system is designated according to the size of the net mouth opening and in two cases, the number of nets it carries. The original MOCNESS (Wiebe et al, 1976) was a redesigned and improved version of a system described by Frost and McCrone (1974).(from MOCNESS manual) This designation is used when the specific type of MOCNESS (number and size of nets) was not specified by the contributing investigator.

Niskin bottle

Supplied Name: Niskin CTD Rosette for seawater

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

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Database

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Dataset: Microorganisms associated with pyrosomes